John Gruber of Daring Fireball fame has written up a piece to try and clear some of the confusion revolving around speed differences noticed by users who save their web apps on the homescreen in iOS 4.3. Specifically, web apps saved to the homescreen are seeing decreased performance when compared to the same web apps being loaded through mobile Safari.
Here’s an excerpt on what he had to say:

The clear insinuation is that web apps running outside Mobile Safari have been made to run slower, but that’s not true. What happened with iOS 4.3 is that web apps (and JavaScript in general) running inside Mobile Safari have been made significantly faster.

The Nitro JavaScript engine is only available within Mobile Safari. Outside Mobile Safari — whether in App Store apps using the UIWebView control, or in true web apps that have been saved to the home screen — apps get iOS’s older JavaScript engine.

Gruber goes on to make his case with a bunch of technical details that I won’t bother repeating here. In sum, it seems that Apple isn’t deliberately hampering web apps, but instead this could simply be an oversight, or an exclusion for another reason. Could we see it in the future? Possibly, but only time will tell.